def set_zooms(self, zooms):
''' Set zooms into header fields
See docstring for ``get_zooms`` for examples
'''
hdr = self._header_data
zooms = np.asarray(zooms)
if len(zooms) != len(hdr['delta']):
raise HeaderDataError('Expecting %d zoom values for ndim' %
hdr['delta'])
if np.any(zooms < 0):
raise HeaderDataError('zooms must be positive')
delta = hdr['delta']
delta[:] = zooms[:]
def __init__(self, binaryblock=None, check=True):
''' Initialize header from binary data block
Parameters
----------
binaryblock : {None, string} optional
binary block to set into header. By default, None, in
which case we insert the default empty header block
check : bool, optional
Whether to check content of header in initialization.
Default is True.
'''
if binaryblock is None:
self._header_data = self._empty_headerdata()
return
# check size
if len(binaryblock) != self.template_dtype.itemsize:
raise HeaderDataError('Binary block is wrong size')
hdr = np.ndarray(shape=(),
dtype=self.template_dtype,
buffer=binaryblock)
#if goodRASFlag, discard delta, Mdc and c_ras stuff
if int(hdr['goodRASFlag']) < 0:
hdr = self._set_affine_default(hdr)
self._header_data = hdr.copy()
if check:
self.check_fix()
return
def _write_data(self, mghfile, data, header):
''' Utility routine to write image
Parameters
----------
mghfile : file-like
file-like object implementing ``seek`` or ``tell``, and
``write``
data : array-like
array to write
header : analyze-type header object
header
'''
shape = header.get_data_shape()
if data.shape != shape:
raise HeaderDataError('Data should be shape (%s)' %
', '.join(str(s) for s in shape))
offset = header.get_data_offset()
out_dtype = header.get_data_dtype()
array_to_file(data, mghfile, out_dtype, offset)
def save(img, filename, dtype_from='data'):
"""Write the image to a file.
Parameters
----------
img : An `Image` object
filename : string
Should be a valid filename.
dtype_from : {'data', 'header'} or dtype specifier, optional
Method of setting dtype to save data to disk. Value of 'data' (default),
means use data dtype to save. 'header' means use data dtype specified
in header, if available, otherwise use data dtype. Can also be any
valid specifier for a numpy dtype, e.g. 'i4', ``np.float32``. Not every
format supports every dtype, so some values of this parameter or data
dtypes will raise errors.
Returns
-------
image : An `Image` object
Possibly modified by saving.
See Also
--------
load_image : function for loading images
Image : image object
Examples
--------
Make a temporary directory to store files
>>> import os
>>> from tempfile import mkdtemp
>>> tmpdir = mkdtemp()
Make some some files and save them
>>> import numpy as np
>>> from nipy.core.api import Image, AffineTransform
>>> from nipy.io.api import save_image
>>> data = np.zeros((91,109,91), dtype=np.uint8)
>>> cmap = AffineTransform('kji', 'zxy', np.eye(4))
>>> img = Image(data, cmap)
>>> fname1 = os.path.join(tmpdir, 'img1.nii.gz')
>>> saved_img1 = save_image(img, fname1)
>>> saved_img1.shape
(91, 109, 91)
>>> fname2 = os.path.join(tmpdir, 'img2.img.gz')
>>> saved_img2 = save_image(img, fname2)
>>> saved_img2.shape
(91, 109, 91)
>>> fname = 'test.mnc'
>>> saved_image3 = save_image(img, fname)
Traceback (most recent call last):
...
ValueError: Sorry, we cannot yet save as format "minc"
Finally, we clear up our temporary files:
>>> import shutil
>>> shutil.rmtree(tmpdir)
Notes
-----
Filetype is determined by the file extension in 'filename'. Currently the
following filetypes are supported:
* Nifti single file : ['.nii', '.nii.gz']
* Nifti file pair : ['.hdr', '.hdr.gz']
* SPM Analyze : ['.img', '.img.gz']
"""
# Try and get nifti
dt_from_is_str = isinstance(dtype_from, basestring)
if dt_from_is_str and dtype_from == 'header':
# All done
io_dtype = None
elif dt_from_is_str and dtype_from == 'data':
io_dtype = img.get_data().dtype
else:
io_dtype = np.dtype(dtype_from)
# make new image
ni_img = nipy2nifti(img, data_dtype=io_dtype)
ftype = _type_from_filename(filename)
if ftype.startswith('nifti1'):
ni_img.to_filename(filename)
elif ftype == 'analyze':
try:
ana_img = nib.Spm2AnalyzeImage.from_image(ni_img)
except HeaderDataError:
raise HeaderDataError('SPM analyze does not support datatype %s' %
ni_img.get_data_dtype())
ana_img.to_filename(filename)
else:
raise ValueError('Sorry, we cannot yet save as format "%s"' % ftype)
return img